Even if the seams are different, the liners looks the same length. I have the same boots. I'll check when I get home to see if they have the same stitching. I have no size difference in mine like you are mentioning. If the sizing is minorly tight, you could go get them baked and pack them out a little.
The inner boots has the same length and perhaps baking them will remove the preassure I feel. But I think not since the placement of the seam is exact where I feel the preassure.
Still no response from the store which is strange because the has previous always been quick in their response.
Great if you can post a picture of your inner boots. Do you have 2012 year model?